Hi again,
Now that I have taken a look at the code, it appears that all images are registered with respect to a single template image.
However, in most situations (at least for the work I do), I have found that alignment is much more accurate if images are aligned in small batches, e.g. 4, and then aligned to the original frame. This follows the philosophy of fg_rigidalign .
The reason is, that over reasonable length image sequences, the atmosphere can evolve and the template does not match features in later images.
Would it be possible to add this feature to sunpy? Happy to develop this functionality.